GPUMD

What is GPUMD?

• GPUMD stands for Graphics Processing Units Molecular Dynamics. It is a general-purpose molecular dynamics (MD) code fully implemented on graphics processing units (GPUs).

• Force evaluation for many-body potentials has been significantly accelerated by using GPUs [1], thanks to a set of simple expressions for force, virial stress, and heat current derived in Ref. [2].

• Apart from being highly efficient, another unique feature of GPUMD is that it has useful utilities to study heat transport [3, 4].

Prerequisites

• You need to have a GPU card with compute capability no less than 3.5 and a CUDA toolkit no older than CUDA 9.0.
• Works for both Linux (with GCC) and Windows (with MSVC) operating systems.

Compile GPUMD

• Go to the src directory and type make. When the compilation finishes, two executables, gpumd and phonon, will be generated in the src directory.

Run GPUMD

• Go to the directory where you can see src.
• Type src/gpumd < examples/input_gpumd.txt to run the examples in examples/gpumd.
• Type src/phonon < examples/input_phonon.txt to run the examples in examples/phonon.

Manual

• We only maintain the online manual now: https://gpumd.zheyongfan.org

Mailing list:

• You can use the following link to subscribe and unsubscribe the mailing list: https://www.freelists.org/list/gpumd

• To post a question, you can send an email to gpumd(at)freelists.org

• Here is the archive (public): https://www.freelists.org/archive/gpumd/

Python interface:

• One of the developers, Alexander J. Gabourie, has written a Python package for pre-processing and post-processing data related to GPUMD. Here is the link: https://github.com/AlexGabourie/thermo

Authors:

• Zheyong Fan (Bohai University and Aalto University; Active developer)
  • brucenju(at)gmail.com
• Alexander J. Gabourie (Stanford University; Active developer)
  • gabourie(at)stanford.edu
• Ville Vierimaa (Aalto University; Not an active developer any more)
• Mikko Ervasti (Aalto University; Not an active developer any more)
• Ari Harju (Aalto University; Not an active developer any more)

Citations

Mandatory citation for any work used GPUMD:

• If you use GPUMD in your published work, we kindly ask you to cite the following paper which describes the central algorithms used in GPUMD:

[1] Zheyong Fan, Wei Chen, Ville Vierimaa, and Ari Harju. Efficient molecular dynamics simulations with many-body potentials on graphics processing units. Computer Physics Communications 218, 10 (2017). https://doi.org/10.1016/j.cpc.2017.05.003

Optional citation to the code repository:

• If you want to cite a link to the GPUMD code you can cite the current Github page: https://github.com/brucefan1983/GPUMD.
• However, if the journal does not accept this citation, you can check the Zenodo page of GPUMD (https://zenodo.org/record/4037256#.X2jkqWj7SUk) and cite the version you used. Each version has a unique DOI, which is very suitable for citation. Remember to change the author list to Zheyong Fan and Alexander J. Gabourie.

Optional citation for the force, heat current, and virial formulas:

• If your work involves using heat current and virial stress formulas as implemented in GPUMD, the following paper can be cited:

[2] Zheyong Fan, Luiz Felipe C. Pereira, Hui-Qiong Wang, Jin-Cheng Zheng, Davide Donadio, and Ari Harju. Force and heat current formulas for many-body potentials in molecular dynamics simulations with applications to thermal conductivity calculations. Phys. Rev. B 92, 094301, (2015). https://doi.org/10.1103/PhysRevB.92.094301

Optional citation for the in-out decomposition for 2D materials:

• You can cite the following paper if you use GPUMD to study heat transport using the in-out decomposition for 2D materials and/or the spectral decomposition method as described in it:

[3] Zheyong Fan, Luiz Felipe C. Pereira, Petri Hirvonen, Mikko M. Ervasti, Ken R. Elder, Davide Donadio, Tapio Ala-Nissila, and Ari Harju. Thermal conductivity decomposition in two-dimensional materials: Application to graphene. Phys. Rev. B 95, 144309, (2017). https://doi.org/10.1103/PhysRevB.95.144309

Optional citation for the HNEMD method and the related spectral decomposition method:

• You can cite the following paper if you use GPUMD to study heat transport using the HNEMD method and the associated spectral decomposition method:

[4] Z. Fan, H. Dong, A. Harju, T. Ala-Nissila, Homogeneous nonequilibrium molecular dynamics method for heat transport and spectral decomposition with many-body potentials, Phys. Rev. B 99, 064308 (2019). https://doi.org/10.1103/PhysRevB.99.064308